rs2844645

Variant names:

• chr6-31047405-G-A
• rs2844645

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.522 in 151,986 control chromosomes in the GnomAD database, including 21,373 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79207 AN: 151866 Hom.: 21333 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.522 AC: 79292 AN: 151986 Hom.: 21373 Cov.: 32 AF XY: 0.514 AC XY: 38157 AN XY: 74258

African (AFR) AF: 0.647 AC: 26817 AN: 41442

American (AMR) AF: 0.424 AC: 6471 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2321 AN: 3464

East Asian (EAS) AF: 0.433 AC: 2238 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3909 AN: 10566

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.490 AC: 33282 AN: 67944

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.504 Hom.: 52582

Bravo AF: 0.530

Asia WGS AF: 0.536 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.7
DANN	Benign	0.91
PhyloP100		-0.012

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2844645; hg19: chr6-31015182;